US11016057B2 - Pulse-field multiplex capillary electrophoresis system - Google Patents
Pulse-field multiplex capillary electrophoresis system Download PDFInfo
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- US11016057B2 US11016057B2 US15/634,846 US201715634846A US11016057B2 US 11016057 B2 US11016057 B2 US 11016057B2 US 201715634846 A US201715634846 A US 201715634846A US 11016057 B2 US11016057 B2 US 11016057B2
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
- G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
- G01N27/416—Systems
- G01N27/447—Systems using electrophoresis
- G01N27/44704—Details; Accessories
- G01N27/44713—Particularly adapted electric power supply
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/1034—Isolating an individual clone by screening libraries
- C12N15/1093—General methods of preparing gene libraries, not provided for in other subgroups
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
- G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
- G01N27/416—Systems
- G01N27/447—Systems using electrophoresis
- G01N27/44704—Details; Accessories
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
- G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
- G01N27/416—Systems
- G01N27/447—Systems using electrophoresis
- G01N27/44704—Details; Accessories
- G01N27/44717—Arrangements for investigating the separated zones, e.g. localising zones
- G01N27/44721—Arrangements for investigating the separated zones, e.g. localising zones by optical means
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
- G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
- G01N27/416—Systems
- G01N27/447—Systems using electrophoresis
- G01N27/44704—Details; Accessories
- G01N27/44743—Introducing samples
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
- G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
- G01N27/416—Systems
- G01N27/447—Systems using electrophoresis
- G01N27/44756—Apparatus specially adapted therefor
- G01N27/44782—Apparatus specially adapted therefor of a plurality of samples
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
- G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
- G01N27/416—Systems
- G01N27/447—Systems using electrophoresis
- G01N27/44756—Apparatus specially adapted therefor
- G01N27/44791—Microapparatus
Definitions
- This invention relates to a system and software for multi-channel pulsed-field capillary electrophoresis.
- next-generation sequencing uses a variety of technologies for sequencing, including pyrosequencing, ion-sequencing, sequencing by synthesis, or sequencing by ligation. Although these technologies have some minor variations, they all have a generally common DNA library preparation procedure, which includes genomic DNA quality & quality assessment, DNA fragmentation and sizing (involving mechanical shearing, sonication, nebulization, or enzyme digestion), DNA repair and end polishing, and a last step of platform-specific adaptor ligation.
- genomic DNA quality & quality assessment includes genomic DNA quality & quality assessment, DNA fragmentation and sizing (involving mechanical shearing, sonication, nebulization, or enzyme digestion), DNA repair and end polishing, and a last step of platform-specific adaptor ligation.
- NGS systems are based on the sequencing of relatively short fragments of poly(nucleic acids), ranging from 30 base-pairs (bp) to 2000 bp in length.
- NGS systems based on pore or nanopore platforms use larger fragment sizes, ranging from 5000 bp or higher. In some cases, the desired fragment sizes are greater than 20,000 to 50,000 bp.
- Newer applications of long-range sequencers target fragment sizes of 50,000 bp to greater than 150,000 bp or longer.
- a labor-intensive step in DNA library preparation is the qualification (size determination) and quantification of both un-sheared genomic DNA and downstream fragmented DNA.
- Existing methods for DNA fragment analysis include agarose gel electrophoresis, capillary electrophoresis, and chip-based electrophoresis.
- Agarose gel electrophoresis is labor intensive, requiring gel preparation, sample transfer via pipetting, and image analysis. The images obtained by agarose electrophoresis are often distorted, resulting in questionable or unreliable data. It is impossible to use agarose gel electrophoresis for accurate quantification of DNA, which means that a separate, second method (UV or fluorescence spectroscopy) is required for quantification.
- PFGE Pulsed-Field Gel Electrophoresis
- PFCE single-capillary pulsed field capillary electrophoresis system
- Sizing results obtained with simple single waveforms on a pulse-field capillary electrophoresis system may give results that are significantly different than results obtained using standard Pulse Field Slab Gel Electrophoresis (PFGE).
- PFGE Pulse Field Slab Gel Electrophoresis
- the average smear size for a DNA smear measured with a single-frequency square-wave capillary electrophoresis system is usually at least 10-20% smaller than what is measured on standard pulsed-field slab electrophoresis systems.
- simple single waveform methods when applied to complex DNA mixtures, often result in anomalous system peaks that don't accurately represent the sample under analysis.
- Multiplex capillary electrophoresis is known.
- Kennedy and Kurt in U.S. Pat. No. 6,833,062 describe a multiplex absorbance based capillary electrophoresis system and method.
- Yeung et al. in U.S. Pat. No. 5,324,401 describe a multiplex fluorescent based capillary electrophoresis system.
- these systems offer the advantage of analyzing multiple samples simultaneously, and can run several plates sequentially, they lack the ability to load or change multiple sample plates while the system is running, and they also lack a simple workflow for efficient sample analysis.
- these multiplex systems lack the ability to measure nucleic acid fragment sizes above about 50,000 bp.
- a limitation of prior-art pulsed-field capillary electrophoresis systems is the lack of an option for environmental temperature control. Temperature can affect run-to-run performance and the long-term reliability of capillary pulse-field systems. Thus, there is a need for a multiplex pulsed-field capillary electrophoresis systems that have an option for carefully controlled environmental temperature control.
- an automated capillary electrophoresis system that a) eliminates the complexity, cost, and required expertise of a robotic system b) enables users to run from one to several thousand samples per day c) allows users to conveniently load several plates or samples onto a capillary electrophoresis system while the system is running other samples d) has the small size and footprint of a stand-alone capillary electrophoresis unit and e) allows users to accurately determine the size of DNA fragments larger than 50,000 bp, and preferably larger than 100,000 bp.
- This invention has, as a primary objective, the fulfillment of the above described needs.
- the present invention is a pulse-field capillary electrophoresis system with the ability to apply a varying or pulsed electric field to at least 2 and preferably at least 12 capillaries simultaneously.
- the present invention also includes application of complex waveforms, which is defined as the application of sequences of simple waveforms that are iterated for the duration of the analytical run.
- a preferred method for obtaining high-quality separations of complex DNA smears using multiplex pulsed-field parallel capillary electrophoresis is to apply different variable voltage waveform patterns, in sequence, over time, in repeated iterations.
- a preferred separation method is to apply a square wave for a period of time followed by a triangle wave for a period of time, and then repeating the square-wave and triangle wave sequence for several iterations. This is shown in FIG. 18A , with a square wave applied for a period of time, T 1 , followed by a triangle wave, applied for a period of time, T 2 .
- the frequency of the applied square wave varies from slow to fast, while the frequency of the triangle wave is constant.
- T 1 +T 2 sequence is iterated for “I” times to obtain a total run time of I(T 1 +T 2 ) minutes.
- Another example is to apply a square wave for a period of time followed by a constant voltage for a period of time, and then iterating the square-wave and constant voltage sequence for several iterations.
- Another preferred aspect of the invention is to apply at least three different waveforms over the period of the electrophoresis separation.
- Another preferred aspect of the invention is to iterate two different waveforms, followed by a third waveform.
- Another example is to apply a square wave, for a first period of time, a constant voltage for a second period of time, and triangle wave for a third period of time, in sequential segments, and iterate the sequence multiple times until the electrophoresis run is complete.
- Another aspect of the invention is a method of applying an electric field across at least two capillaries, comprising; applying a first pulse-field waveform at a first frequency across said capillaries for a first period of time; applying at least a second, different shape pulse-field waveform at a second frequency across said capillaries for a second period of time; and thereafter repeating the said first and at least second pulse-field waveforms at least twice; wherein said first frequency varies with time within said first period of time and said second frequency varies with time within said second period of time.
- FIG. 1 shows a left-front-view of the instrument, with 6 drawers for holding sample and buffer plates.
- FIG. 2 shows a right-front view of the instrument with one drawer pulled out for placement of a buffer plate and the top and side door compartments open.
- FIG. 3 shows the x-z stage assembly
- FIG. 4 shows a drawer, stage assembly, tray holder, and sample plate.
- FIG. 5 shows the bottom of a tray holder.
- FIG. 6 shows a right-side view of the instrument without the cover.
- FIG. 7 shows the left-side view of the instrument without the cover.
- FIG. 8 shows a capillary array cartridge
- FIG. 9 shows the flow-chart for the software control program for creating a queue of jobs.
- FIG. 10 shows a computer screen image of the computer software.
- FIG. 11 shows the positioning of a sample plate under the array by the stage.
- FIG. 12A shows a view of the capillary electrophoresis reservoir system.
- FIG. 12B shows a view of the capillary electrophoresis reservoir system.
- FIG. 13A shows a view of the x-z stage relative to the drawers.
- FIG. 13B shows a view of the x-z stage with a sample tray lifted.
- FIG. 14 shows a back view of the instrument with a pulse-field power supply.
- FIG. 15A shows a top view of the instrument with a temperature control chamber.
- FIG. 16A shows a prior-art slab-gel separation of Marker 7GT
- FIG. 16B shows the separation of Marker 7GT using prior-art capillary electrophoresis with constant applied electric field.
- FIG. 16C shows the separation of Marker 7GT using the capillary electrophoresis system of the present invention with a pulsed applied electric field.
- FIG. 18A shows an example of a square wave applied for a period of time T 1 , followed by a triangle wave applied for a time T 2
- FIG. 18B shows an example of a sine wave applied for a period of time T 1 , followed by a square wave applied for a time of T 2 .
- the invention is a multiplexed pulsed-field capillary electrophoresis system with enhanced workflow.
- the capillary electrophoresis system and apparatus of the present invention includes an absorbance or fluorescence-based capillary electrophoresis sub-system with a light source, a method for carrying light from the light source to the sample windows of a multiplex capillary array containing at least 12 capillaries (preferably 96 capillaries), and a method for detecting light emitted (fluorescence) or absorbed (absorbance) from the sample windows of a multiplex array.
- the sub-system also includes a method for pumping buffers and gels through the capillaries, as well as a method for application of an electric field for electrophoretic separation.
- the optics of the fluorescent-based sub system of the present invention are described by Pang in United States Patent Applications 20070131870 and 20100140505, herein incorporated by reference in their entirety.
- the optics of an applicable absorbance-based system, as well as the fluid handling, reservoir venting, application of electric field, and selection of fluids via a syringe pump and a 6-way distribution valve are discussed by Kennedy et al. in U.S. Pat. Nos. 7,534,335 and 6,833,062, herein incorporated by reference their entirety.
- the multiplex capillary system (or unit or instrument) and/or console 16 has a door 10 for easy access to the loading of gels, two drawers 11 for the easy loading of a buffer tray and a waste tray.
- Drawers 12 can be opened for easy loading of 96 well PCR plates, tube strips, vials, or other sample containers.
- a top door 13 can be opened to access a replaceable capillary array, array window, and capillary reservoir.
- An indicator light 14 is used to for notifying users of the active application of a high-voltage for electrophoresis.
- a removable back-panel 15 allows access to electronics such as a high-voltage power supply, electrical communication panels, a pump board, pressure transducer board, and stage driver electronics. The back panel 15 also allows maintenance access to the x-z stage, which is used to move sample trays from the drawers 11 and 12 to a capillary array.
- a vent valve 21 is connected to the top of a capillary reservoir 20 .
- a syringe pump 23 coupled with a 6-way distribution valve 29 delivers fluids and electrophoresis gels from fluid containers 24 and 25 into the capillary reservoir 20 , waste container 26 , or capillaries in the capillary array 17 .
- a fan 27 is used for forcing cool air from the back compartment through the capillary array 17 , past the outside of the capillary reservoir 20 , down past the fluid containers 24 , 25 and finally out the bottom of the instrument.
- LED indicator lights 120 are used to indicate the presence or absence of trays in the drawers.
- a buffer tray 28 is shown in a drawer ( 11 , FIG. 1 ).
- the capillary array reservoir tip 91 is shown inserted into the capillary reservoir 20 .
- FIG. 3 shows the x-z stage assembly 48 , which is used to transport sample plates or trays ( 50 , FIG. 4 ) and associated tray holders ( 51 , FIG. 4 ) from the drawers ( 12 FIG. 1 ) to the injection capillaries ( 72 , FIG. 8 ) and injection electrodes ( 71 , FIG. 8 ) of the capillary array ( 17 , FIG. 8 ).
- the x-z stage assembly 48 is also used to position a buffer tray or waste tray ( 28 , FIG. 2 ) from the drawers ( 11 , FIG. 1 ) to the injection capillaries 72 and injection electrodes 71 of the capillary array 17 ( FIG. 8 ).
- the x-z stage assembly 48 has a tray carrier 31 with alignment pins 32 , which align with holes ( 57 , FIG. 5 ) on the bottom of the tray holder ( 51 , FIG. 4 ) to prevent subsequent sliding or movement of the tray holders 51 during transport.
- a protective cover 34 made of metal or plastic, is used to prevent gels or other liquids from spilling onto the x-direction guide rails 38 and x-direction drive belt 37 of the x-z stage assembly 48 .
- An x-drive stepper motor 35 is used as the electro-mechanical driver for motion in the x-direction.
- a drive pulley 36 is attached to the stepper motor 35 and x-direction drive belt 37 which drives the stage carrier 39 back-and forth along the guide-bars 38 .
- a second drive pulley (not shown) is used on belt 37 towards the back-end of the stage, which allows the belt 37 to make a full loop when affixed to stage carrier 39 .
- Any motor-induced movement of the belt 37 induces an x-direction movement of the stage carrier 39 on the guide rails 38 .
- a stepper-motor for the z-position is located at 41 , which is attached to a drive pulley/belt configuration similar to that shown in the x-direction.
- the z-direction drive belt is shown as 43 .
- the z-position motor/pulley/belt is used to move the tray carrier 31 up and down the guide bars 40 .
- Top plate 33 serves as a structural support for the guide bars 40 .
- An electrical communication strip 44 is used to communicate between an electrical motor control board 46 and the stepper motors 41 and 35 .
- An x-direction membrane potentiometer strip 49 along with appropriate control electronics, is used to determine and control the absolute position of the stage carrier 39 in the x-direction.
- a z-direction membrane potentiometer strip 42 along with appropriate control electronics, is used to determine the absolute position of the tray carrier 31 in the z-direction.
- Linear encoders or rotational encoders (on the stepper motor 35 , 41 ) are alternative forms of positional measurement and control.
- Bearings 45 are located on each guide bar 40 and guide rail 38 to enable friction-free movement of both the tray carrier 31 and the stage carrier 39 . Note that there are two guide bars 40 or guide rails 38 per axis. Electrical cord guide straps 47 are attached to a back support, which also holds the electrical control board 46 for the x-z stage assembly 48 .
- FIG. 6 Shows a right side view of the electrophoresis system, with a chassis 66 , pump motor and control system 61 , pump control board 62 , LED light engine 69 , LED light line 67 , high voltage power supply board 65 , capable of applying 0.0 kV to 15 kV across the electrodes of the capillary array 17 , a CCD camera 64 , capillary array cartridge 17 , array window holder 19 , capillary reservoir 20 , drawers 11 , drawers 12 , fluid lines 68 , waste container 26 , gel containers 25 and syringe 23 .
- a USB electronic distribution bard is shown as 63 .
- FIG. 7 shows a left side-view of the electrophoresis unit 16 showing the x-z stage assembly 48 , which moves tray holders 51 and sample trays or plates 50 from a drawer 12 or 11 to the bottom of the capillary array 17 .
- the stage unit 48 can move the sample tray holder 51 and sample tray 50 up in the z-direction to lift the tray holder/sample tray off of the drawer 12 (or 11 ), move back in the x-direction away from the sample drawers 12 , and then move the sample plate 50 up in the z-direction to the bottom of the capillary array 17 .
- the stage unit 48 can move the sample tray holder/sample tray back down to the target drawer position (down in the z-direction), move forward in the x-direction just above the sample plate 50 , and then drop down in the z-direction to set the sample tray holder/sample tray onto the drawer 12 .
- the sample tray holder 51 is resting in a drawer 12 , the back edge of the sample tray holder 51 and sample tray 50 are aligned so that they do not lie directly underneath the capillary array 17 . This allows the sample stage tray carrier ( 31 , FIG.
- the alignment pins ( 70 , FIG. 8 ) on the bottom of the capillary array 17 are used to align the tray holder 51 with a sample tray 50 so that the capillary and electrode tips (the tips of the injection capillaries 72 and the injection electrodes 71 ) dip into each sample well of the sample plate 50 and do not collide with other areas of the sample plate 50 .
- FIG. 11 shows a sample tray holder 51 with a sample tray 50 aligned underneath a capillary array 17 .
- Alignment holes 56 on the tray holder 51 force the alignment of the tray holder 51 with the capillary array alignment pins 70 .
- FIG. 7 also shows high voltage power supply board 65 and high voltage power supply cable 75 (to the capillary array 17 ).
- FIG. 8 shows a capillary array cartridge 17 , with rigid plastic support structure 77 , window storage and transport screw 80 , capillary support cards 76 , high voltage power supply cable 75 , and insulating support structure 73 onto which the electric circuit board 74 is placed. Electrodes 71 protrude through the electric circuit board 74 , through the insulating support structure 73 , and protrude through the bottom of the capillary array 17 .
- the electrode material is stainless steel or tungsten.
- the electrode dimension, which is not a critical aspect of the invention, is 50 mm diameter by 29 mm length.
- the protrusion from the bottom of the cartridge base is 20.0 mm.
- the electrodes 71 are soldered onto the circuit board 74 .
- the high voltage power supply cable 75 is also soldered to the same circuit of the electrical circuit board 74 , which enables contact of the electrodes 71 with the high voltage power supply ( 65 , FIG. 6 ).
- Capillary tips (the tips of the injection capillaries 72 ) are threaded through the electric circuit board 74 and insulated support structure 73 and are aligned immediately adjacent and parallel to the electrode tips (the tips of the injection electrodes 71 ).
- the distance between the capillary tips and electrode tips are from 0.1 mm to 4 mm.
- the ends of the capillary tips and the ends of the electrode tips lie in a single plane (i.e. the capillary tips and electrode tips are the substantially the same length, with length variation of no more than about +/ ⁇ 1 mm.
- the length variation of capillary tips and electrode tips is less than 0.5 mm.
- the capillaries 72 thread through the bottom of the capillary array 17 , through the insulating support structure 73 , through the electric circuit board 74 , through the capillary support cards 76 (which are supported by the rigid plastic support structure 77 ) through the capillary window holder 78 with capillary windows 79 centered in the opening of the window holder 78 , and then finally through the capillary reservoir tip 91 , in which all capillaries 72 (in this case 12 ) are threaded through a single hole.
- capillaries 72 are threaded in groups of 12, or preferably groups of 4 in the capillary reservoir tip 79 .
- the capillaries 72 are held in place in the reservoir tip 91 with an adhesive, such as a thermally or UV-curable epoxy.
- FIG. 12A shows the capillary reservoir 20 , with reservoir body (indicated by the arrow of 20 ), capillary reservoir tip 91 , slider bar 130 (for locking capillary reservoir tip 91 into the capillary reservoir 20 , through alignment of a notch on the capillary reservoir tip 91 and the slider bar 130 ), vent block valve 21 , waste tube out 138 , waste block valve 132 , and pressure transducer cavity 133 .
- FIG. 12B shows an alternate cut-out view of the capillary reservoir 20 , with the reservoir body, capillary reservoir tip 91 , slider bar 130 , vent block valve 21 , waste tube out 138 , waste block valve 132 , electrode for attachment to ground (or ground electrode) 135 , pressure transducer cavity 133 , pressure transducer 136 , pressure transducer cable for attachment to analog/digital board 137 , and fluid tube input 134 (from syringe pump 23 FIG. 2 ).
- the reservoir body of the capillary reservoir 20 can be made of any solid material such as acrylic, Teflon, PETE, aluminum, polyethylene, ABS, or other common metals or plastics.
- the key criterion is that the material is durable and chemically resistant to the materials used.
- a preferred material is acrylic or Teflon.
- FIG. 13A shows the x-z stage unit 48 in relation to the drawers 11 and 12 .
- the x-z stage is located directly behind the drawers 11 and 12 , and can move the stage carrier ( 39 , FIG. 13B ) back-and forth in the x-direction using the stepper-motor for the x-position ( 35 , FIG. 3 ).
- a sample tray 50 is removed from a drawer 12 (or 11 ) by first moving the stage forward, towards the drawers 11 and 12 , in the x-direction.
- the tray carrier ( 31 , FIG. 3 ) lifts a tray holder 51 up and off a drawer 12 in the z-direction using the z-direction stepper motor 41 (see also FIG. 3 ).
- the stage carrier 39 is then moved back in the x-direction, away from the drawers 11 and 12 , as shown in FIG. 13B .
- the stage carrier 39 is then moved up in the z-direction to move the tray holder 51 and sample tray 50 to the injection position of the capillary array 17 ( FIG. 11 ).
- a typical strategy for pumping fluids for capillary electrophoresis is as follows. Consider the following 6 positions of the six-way distribution valve ( 29 , FIG. 2 ) on the syringe pump 23 . Position 1 is connected to the bottom of the capillary reservoir 20 (fluid tube input 134 , FIG.
- position 2 is connected through a tube to a bottle of conditioning fluid (a fluid for conditioning the walls of the capillaries 72 );
- position 3 is connected to a “Gel 1 ” which is used for the analysis of genomic DNA,
- position 4 is connected to a “Gel 2 ” which is used for the analysis of fragmented DNA,
- position 5 is unused, or optionally used to clean the vent valve via the pumping of air through the vent valve to the waste bottle and position 6 is connected to the waste bottle 26 .
- Step A The capillary reservoir 20 is first emptied by opening position 1 (reservoir), filling the syringe 23 with fluid that is in the capillary reservoir 20 , closing position 1 , opening position 6 , and emptying fluid to the waste (waste container 26 ). This is repeated until the capillary reservoir 20 is empty. Block valves 21 and 132 are kept open during this process to enable efficient draining of the capillary reservoir 20 .
- Step B The capillary reservoir 20 is then filled with conditioning solution by opening position 2 , filling the syringe 23 with conditioning solution, closing position 2 , opening position 1 , and filling the capillary reservoir 20 with conditioning solution.
- Block valve 21 is closed, but block valve 132 to waste (waste container 26 ) is open, enabling the over-filling of the capillary reservoir 20 with conditioning solution.
- Step C The capillaries 72 are filled by closing both vent block valve 21 and waste vent valve 132 .
- the syringe 23 is filled with capillary conditioning solution.
- Position 1 is opened, and fluid is pressure filled through the capillaries 72 at a minimum of 100 psi for a pre-determined time, which may range from 1 minute to 20 minutes.
- Step D The capillary reservoir 20 is emptied by step A, and then re-filled with gel using the same process as in Step B, except that position 3 for the gel is used on the 6-way distribution valve 29 .
- Step E The capillaries 72 are filled with gel using a process analogous to Step C.
- the capillaries 72 are ready for electrophoresis.
- a general strategy and process for analyzing samples using electrophoresis is as follows.
- Samples are placed into a 96-well plate (sample tray or plate 50 ) for analysis.
- the user places the sample plate 50 into a sample drawer ( 12 , FIG. 1 ), and then adds jobs to a computer-based queue, corresponding to the analysis of a specific row or the entire sample plate 50 in the drawer 12 .
- the computer which is the control system of the instrument, executes the analysis of the row or entire sample tray 50 of interest.
- a key embodiment of the invention is the workflow of the capillary electrophoresis system.
- Drawers 11 , FIG. 1
- Drawers 12 , FIG. 1
- Drawers allow easy placement of sample trays into the system 16 .
- Of particular importance is the ability to place or remove sample trays 50 from drawers ( 12 , FIG. 1 ) while the system 16 is performing capillary electrophoresis.
- Indicator lights 120 , FIG. 1 ) show if a tray 28 , 50 is present or absent in a drawer 11 , 12 , which let users know if a drawer 11 , 12 is in place.
- a typical workflow for a 12-capillary multiplex system is as follows: User A walks up to the machine with sample tray 1 , and places it into the third drawer from the top (one of drawers 12 , FIG. 1 ). User “A” then fills a queue with three jobs, which correspond to performing capillary electrophoresis on the three rows of samples: sample tray 1 row A, sample tray 1 row B, and sample tray 1 row C. User “A” then instructs the computer to execute the queue, and as a result, the system begins capillary electrophoresis of sample tray 1 , row A, and will continue executing jobs in the queue until there are no more jobs. User “B” then comes up and places sample tray 2 into the fourth drawer from the top (one of drawers 12 , FIG.
- FIG. 1 It is, among other things, the enabling of this workflow, via the drawers 11 and 12 , sample stage (x-z stage assembly 48 ), and computer program with a queue for loading jobs that differentiates the present invention from the prior art systems for CE workflow.
- An important embodiment of the present invention is a computer program that enables users to load a sample plate 50 into the desired vertical drawer ( 12 , FIG. 1 ), and instruct the system 16 to run the desired rows or entire sample plate 50 , while the system 16 is running other samples. This allows multiple users to load samples and/or sample plates 50 , or a single user to load multiple samples and/or sample plates 50 without first having to wait for the electrophoresis of other samples to be complete.
- FIG. 9 shows the general flow diagram of the work process and computer program.
- a user loads a sample tray 50 into a drawer ( 12 , FIG. 1 ) of the system 16 .
- the user selects the sample tray 50 , and edits the sample names and/or tray name.
- the user further selects or defines a method (time of separation, electric field used for separation, gel selection, etc.).
- This selected sample tray 50 along with an associated method is defined as a “job”, which is then placed into a queue.
- the computer as an instrument control device, fetches jobs from the queue, and controls the instrument (system 16 ) for every task, including operation of the syringe pump 23 , operation of the high voltage power supply 65 , and the motion control stage ( 48 , FIG. 3 ).
- Tasks associated with control of the syringe pump 23 include emptying/filling the capillary reservoir 20 with conditioning fluid, and forcing conditioning fluid through the capillaries 72 , emptying/filling the capillary reservoir 20 with gel, and forcing gel through the capillaries 72 .
- Tasks associated with control of the x-z stage assembly 48 may include moving or removing a waste tray to/from the inlet side of the capillaries 72 and electrodes 71 of the capillary array 17 , moving or removing a buffer tray 28 to/from the inlet capillaries and electrodes of the capillary array, or moving/removing a sample tray to/from the inlet side of the capillaries 72 and electrodes 71 of the capillary array 17 .
- Tasks associated with control of the high voltage power supply 65 include turning off/on a high voltage for capillary electrophoresis separation. Other tasks are associated with the camera 64 (acquisition of data), and block valves 21 and 132 .
- the program For each set of samples, the program will complete all tasks required to obtain a set of electropherograms. Once these tasks are complete, the program fetches another job from the queue. If the queue is empty, all sample runs are complete (until the user initiates another queue).
- FIG. 10 The graphical result of this computer program is shown in FIG. 10 , which shows a list of samples to be analyzed in queue 101 , an option to add rows or sample trays 50 to the queue 102 , and an option to select the tray number for analysis 103 .
- a) Selection of tray 103 (corresponding to a drawer 11 FIG. 1 )
- Another critical aspect is the ability to add samples to instrument drawers ( 11 , 12 FIG. 1 ) and queue ( 101 , FIG. 10 ) while the instrument (system 16 ) is running other samples.
- FIG. 14 shows a back view of the instrument with a pulse-field high voltage (HV) power supply 141 , control electronics 143 , and a cooling fan 142 to remove heat generated by the power supply 141 .
- Pulsed field voltage power supply 141 with cooling fan 142 replaces constant-field power supply 65 shown in FIG. 6 .
- a preferred pulse-field power supply is a UltravoltTM 20HVA24-BP2,15HVA24-BP2, or 10HVA24-BP2.
- the output of the power supply 141 is controlled by a control board 143 with variable control voltage.
- a non-limiting example is a variable control voltage range between plus 10V and minus 10V.
- the plus 10 V and minus 10 V is scaled to the output of the power supply 141 .
- the application of a plus 10 V control voltage delivers plus 10 kV from the power supply 141
- the application of a minus 10V control voltage delivers minus 10 kV from the power supply 141
- An application of plus 5 V to this same 10 kV power supply 141 results in an output voltage of plus 5 kV.
- the application of a plus 10V control voltage delivers a plus 20 kV from the power supply 141
- an application of plus 5 V results in plus 10 kV voltage from the power supply 141 .
- the control voltage and the associated scaling factor linked with the output of the pulsed-field power supply 141 may be different than the example described above, and is not a critical component of the invention.
- a waveform generator which is also a part of control board 143 , produces the complex waveforms that result in the variable voltage output of the pulsed-field power supply 141 .
- a plus 7V/minus 4V 10 Hz square wave on the control voltage results in a plus 7 kV/minus 4 kV 10 Hz (Pulse Power) output of the HV pulse power supply 141 .
- the output at one end of the pulsed HV power supply 141 is attached to a multiplex capillary array circuit board 74 through the HV power supply cable 75 as shown in FIG. 8 .
- the output of the return path of the pulsed HV power supply 141 is attached to the outlet electrode (electrode on the reservoir side of the capillaries), which is also connected to ground (or ground electrode) 135 ( FIG. 12B ).
- An embodiment of the present invention is the application of a pulse-field power supply 141 to a multiplex capillary electrophoresis system 16 containing at least two and preferably 12 capillaries 72 , so that all capillaries 72 of the multiplex capillary array 17 receive approximately the same pulsed electric field.
- Another embodiment includes the application of a pulse-field power supply 141 to a capillary electrophoresis system 16 containing at least 24 capillaries 72 .
- An on-board processor e.g., control electronics or board 143
- the frequency of the waveform can vary anywhere from ⁇ 1 Hz to 100 Hz.
- a preferred frequency range is from 1 Hz to 50 Hz. Another preferred range is from 1 Hz to 20 Hz. An especially preferred range is from 2 Hz to 10 Hz.
- the control board 143 also has voltage and current monitoring circuitry, so that the voltage applied to the capillary electrophoresis system 16 is actively monitored.
- FIG. 15A shows a top view of the instrument (system 16 ) with a temperature control chamber 150 with a Peltier cooler 151 and a fan 152 for removing the external heat generated by the Peltier cooler 151 .
- An example Peltier Cooler 151 of the present invention is CP14,127-045 (part number 66101-500) made by Lair Technologies.
- FIG. 15B shows a top view of the instrument (system 16 ) with the temperature control chamber 150 with a cutout view, showing the capillary array 154 , and internal heating element and air fan 153 , which when combined with Peltier cooler 151 enables precise control of the temperature from 10 C. to 25 C.
- applying waveforms is equivalent to “applied electric fields”. Applying varying pulse-field waveforms across at least two capillaries is identical to applying a pulse-electric field across at least two capillaries.
- Anode a positively charged electrode relative to the cathode.
- the anode may be at a ground voltage, but positive relative to the cathode.
- Cathode a negatively charged electrode, relative to the anode.
- the cathode may optionally be at a ground voltage, but negative relative to the anode.
- Higher pulse voltage the highest applied voltage of an alternating or varying voltage, over a single cycle of the applied voltage.
- Lower pulse voltage the lowest applied voltage of an alternating or varying voltage, over a single cycle of the applied voltage.
- Simple single waveforms are a single waveform shape applied with fixed frequencies and voltages, or optionally varying frequencies and voltages.
- a simple waveform may consist of a pure sine-wave, with a frequency varying from 50 Hz to 10 Hz over a 60-minute period.
- a simple waveform may also have asymmetric applied voltage.
- An example is a square wave with an applied voltage of plus 3 kV to minus 7 kV.
- a simple waveform may also have varying voltages over time.
- a sine wave may have higher pulse voltage that may ramp linearly from plus 10 kV to minus 3 kV over a period of time, T, while the lower pulse voltage may ramp linearly from minus 5 kV to minus 1 KV over the same period of time.
- Simple waveforms may also have a forward direction pulse that is identical in time to the reverse-direction pulse. For example, a square wave with plus 5 kV forward pulse of 1 second and minus 6 kV reverse pulse of 1 second. Simple waveforms may also have a forward direction pulse that is different in time to the reverse-direction pulse. For example, a square wave with a plus 5 kV forward pulse of 2 second and minus 6 kV reverse pulse of 1 second.
- Simple waveforms may have a duration of the higher pulse voltage longer or shorter than the duration of the lower pulse voltage.
- a 50% duty cycle would define a higher pulse voltage time (T 1 ) equal to a lower pulse voltage time (T 2 ).
- the relative duty of the positive pulse is (T 1 *100/(T 1 +T 2 )).
- T 1 T 2
- the duty cycle is 50%.
- a plus/minus 5 kV 1 Hz square wave applied to an electrophoresis column may have 0.66 seconds at plus 5 kV and 0.33 seconds at minus 5 kV for a 66% duty cycle.
- One aspect of the present invention is the application of complex waveforms, which is defined as the application of sequences of simple waveforms that are iterated for the duration of the analytical run.
- a preferred method for obtaining high-quality separations of complex DNA smears using multiplex pulsed-field parallel capillary electrophoresis is to apply different variable voltage waveform patterns, or simple waveforms, in sequence, over time, in repeated iterations.
- a preferred separation method is to apply a square wave for a period of time followed by a triangle wave for a period of time, and then repeating the square-wave and triangle-wave sequence for several iterations. This is shown in FIG. 18A , with a square wave applied for a period of time, T 1 , followed by a triangle wave, applied for a period of time, T 2 .
- T 1 a period of time
- T 2 a triangle wave
- FIG. 18A shows a sine wave (fixed frequency) applied for a period of time, T 1 , followed by a square wave of varying frequency for a period of time T 2 .
- T 1 +T 2 sequence is iterated for “I” times to obtain a total run time of I(T 1 +T 2 ) minutes.
- Another example is to apply a square wave for a period of time followed by a constant voltage for a period of time, and then iterating the square-wave and constant voltage sequence for several iterations.
- Another preferred aspect of the invention is to apply at least three different waveforms over the period of the electrophoresis separation.
- Another preferred aspect of the invention is to iterate two different waveforms, followed by a third waveform.
- Another example is to apply a square wave, for a first period of time, a constant voltage for a second period of time, and triangle wave for a third period of time, in sequential segments, and iterate the sequence multiple times until the electrophoresis run is complete.
- Another preferred method for obtaining high-quality separations is to apply different waveform patterns over time, and apply a varying frequency or varying voltage ramp, or a combination of both, to the electrophoretic separation.
- Another preferred method uses shorter periods of time for the frequency ramp. For example, a square wave varying from plus 250 V/cm to minus 100 V/cm with a frequency ramp of 15 Hz down to 0.5 Hz over a period of 30 seconds, followed by a Triangle wave varying from plus 250 V/cm to minus 100 V/cm with a frequency ramp of 10 Hz to 5 Hz over a period of 30 seconds, with the square/triangle wave sequence iterated 90 times for a total run time of 90 minutes.
- the time range for each applied wave form varies from 0.5 seconds up to 20 minutes.
- a preferred range is from 15 seconds to 10 minutes.
- An even more preferred time frame is from 10 seconds to 120 seconds.
- the frequency range for each applied wave form varies from 100 Hz to 0.5 Hz.
- a preferred frequency range is from 30 Hz to 0.5 Hz.
- Another preferred range is from 20 Hz to 2 Hz. It is preferable to ramp the frequency over the time period of each applied waveform. For example, if a square wave is applied for 1 minute, the frequency is ramped from 2 Hz to 15 Hz or from 15 Hz to 2 Hz over the same 1 minute timeframe.
- the output of the pulsed-field HV power supply is connected to the inlet electrodes through circuit board 74 (the set of electrodes on the sample or buffer tray side of the capillary array) as shown in FIG. 8 , whereas the outlet electrode (electrode on the reservoir side of the capillaries) is connected to ground 135 FIG. 12B , which is also the return path of the pulsed-field HV power supply.
- a preferred process for performing multiplex capillary electrophoresis of the present invention is to fill at least two capillaries 72 with conductive medium containing a sieving matrix, introduce a sample into the capillaries 72 through either electrokinetic injection or hydrodynamic injection (i.e. by vacuum injecting or pressure injecting a sample into the capillaries 72 ), apply a varying voltage of the present invention via a pulse-field power supply across the capillaries 72 to induce separation of the sample, and then detect the sample as it passes through the windows 79 of the capillaries 72 by fluorescence or absorption detection.
- One preferred method of applying a varying electric field across at least two capillaries comprises; applying a first pulse-field waveform at a first frequency across said capillaries for a first period of time; applying at least a second, different shape pulse-field waveform at a second frequency across said capillaries for a second period of time; thereafter repeating the said first and at least second pulse-field waveform at least twice; wherein said first frequency varies with time within said first period of time and said second frequency varies with time within said second period of time.
- a pulse-field capillary electrophoresis gel “930 Gel” (available from Advanced Analytical Technology) was used for this example.
- the “930 Gel” sieving matrix was pumped into a plurality twelve capillaries with an effective length of 22 cm and a total length of 40 cm (50 um I.D.) using the capillary electrophoresis system described in this specification.
- a 7GT DNA sizing ladder (Available from Wako Chemical Company) comprised of DNA fragments with sizes of 10.06 kB, 17.7 kB, 21.2 kB, 23.45 kB, 41.77 kB, 50.31 kB, and 165.65 kB ( FIG.
- FIG. 16A was used to evaluate separation efficiency on a capillary electrophoresis system.
- a sample of 150 pg/ ⁇ L of the 7GT ladder in 1 ⁇ TE Buffer was prepared as a sample for analysis.
- the gel-filled capillaries were treated with an electrophoresis pre-run by applying 2.0 kV for 1 second prior to injection of sample.
- the 7GT ladder sample was injected onto the capillary electrophoresis system (present invention) using an electrokinetic injection of 5 kV for 5 sec. This was immediately followed by an electrophoresis run using a constant applied voltage of 7.2 kV for 3600 seconds, with the resulting electropherogram shown in FIG. 16B .
- a pulse-field capillary electrophoresis gel “FP 5001 Large DNA Separation Gel” (available from Advanced Analytical Technology) was used for this example.
- the “FP 5001 Large DNA Separation Gel” sieving matrix was pumped into a plurality twelve capillaries with an effective length of 22 cm and a total length of 40 cm (50 um I.D.) using the capillary electrophoresis system described in this specification.
- a 7GT DNA sizing ladder (Available from Wako Chemical Company) comprised of DNA fragments with sizes of 10.06 kB, 17.7 kB, 21.2 kB, 23.45 kB, 41.77 kB, 50.31 kB, and 165.65 kB ( FIG.
- FIG. 16A was used to evaluate separation efficiency on a capillary electrophoresis system.
- a sample of 150 pg/ ⁇ L of the 7GT ladder in 1 ⁇ TE Buffer was prepared as a sample for analysis by dilution in 0.25 ⁇ Tris-EDTA buffer.
- the gel-filled capillaries were treated with an electrophoresis pre-run by applying 2.0 kV for 1 second prior to injection of sample.
- the 7GT ladder sample was injected onto the capillary electrophoresis system (present invention) using an electrokinetic injection of minus 5 kV for 5 sec. This was immediately followed by an electrophoresis run using two different conditions.
- FIG. 17A (Top trace- 1704 ) was obtained using an applied voltage consisting of a Triangle Wave (plus 2.0 kV to minus 7.2 kV) with a frequency of 2 to 7 Hz, varied linearly over a period of 30 seconds, followed by a square wave (plus 2.0 kV to minus 7.2 kV) with a frequency of 2 to 7 Hz, varied linearly over a period of 30 seconds.
- the Triangle wave (30 seconds) followed by Square wave (30 seconds) was iterated for 100 times for a total run time of 100 min.
- bottom trace 1705 was obtained using an applied voltage consisting of a Square Wave (plus 2.0 kV to minus 7.2 kV) with a frequency of 2 to 7 Hz, varied linearly over a period of 30 seconds.
- the Square wave (30 seconds) was iterated for 200 times for a total run time of 100 min.
- the fragment separation was similar for both the top trace and the bottom trace, indicating that the application of the iterated triangle/square waveform ( FIG. 17A top trace) did not substantially affect the separation of the 7GT fragments, as compared to a pure square-wave method without iterations ( FIG. 17A lower trace).
- a gDNA sample (Sample A) was diluted to 150 pg/ ⁇ L in 0.25 Tris-EDTA buffer.
- the gel-filled capillaries were treated with an electrophoresis pre-run by applying 2.0 kV for 1 second prior to injection of sample.
- Sample A was injected onto the capillary electrophoresis system (present invention) using an electrokinetic injection of minus 5 kV for 5 sec. This was immediately followed by an electrophoresis run using two different conditions.
- Race 1701 was obtained using an applied voltage consisting of a Triangle Wave (plus 2.0 kV to minus 7.2 kV) with a frequency of 2 to 7 Hz, varied linearly over a period of 30 seconds, followed by a square wave (plus 2.0 kV to minus 7.2 kV) with a frequency of 2 to 7 Hz, varied linearly over a period of 30 seconds.
- the Triangle wave (30 seconds) followed by Square wave (30 seconds) was iterated for 100 times for a total run time of 100 min.
- Track 1702 was obtained using an applied voltage consisting of a Square Wave (plus 2.0 kV to minus 7.2 kV) with a frequency of 2 to 7 Hz, varied linearly over a period of 30 seconds. The Square wave (30 seconds) was iterated for 200 times for a total run time of 100 min. Note that the trace 1701 had a much higher average smear size of 73,692 bp vs. trace 1702 with an average smear size of 53,478 bp. Also, the trace 1701 ( FIG. 17B ) obtained with the triangle/square iterated blend shows no anomalous system peak 1703 ( FIG. 17B ). The actual size of Sample A is roughly 70 kpb as determined by normal Pulse-Field slab gel electrophoresis, which matches the results obtained with the pulse-field capillary system of the present invention.
- the pulsed-field multiplex capillary electrophoresis system of the present invention allows for the multiplexed, enhanced separation of fragments with sizes up to >150 kB, compared to prior-art constant-field multiplex capillary electrophoresis systems.
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EP18743216.6A EP3646020A1 (en) | 2017-06-27 | 2018-06-27 | Pulse-field multiplex capillary electrophoresis system |
CN201880041935.0A CN110785658B (en) | 2017-06-27 | 2018-06-27 | Pulse field multiple capillary electrophoresis system |
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